NIN p.Val1230=
c.3690G>A · rs751816750 · VCV2069223
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0265%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.048 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.093 | GERP -2.2, phastCons 0.34 |
| Overall | ||
| CADD | 3.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0265%
European (non-Finnish) · 313/1,179,916 alleles
Filtering AF
0.0241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0231%
Overall
0.02%
322/1,613,598 alleles · ultra-rare
exomes 308/1,461,490 · genomes 14/152,108 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0265% | 3,770 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,494 |
| African / African-American | 0.00535% | 18,702 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NIN
- Protein
- p.Val1230=
- Coding
- c.3690G>A
- MANE Select
- NM_020921
- dbSNP
- rs751816750
- Type
- single nucleotide variant
- Location
- chr14:50757340 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.47
- Residue 1230
- the 'important for interaction with cep170' region; the 'interacts with dsp' region
Similar variants
- NIN p.Val1230Leu Uncertain significance ★ ⚠ same residue
- NIN p.Arg2039Ter Likely pathogenic ★★ same type
- NIN p.Ala1049Thr Uncertain significance ★★ ⚠ same type
- NIN p.Ala1212Val Uncertain significance ★★ ⚠ same type
- NIN p.Ala1350Gly Uncertain significance ★★ ⚠ same type
- NIN p.Ala1741Val Uncertain significance ★★ ⚠ same type
- NIN p.Ala1755Thr Uncertain significance ★★ ⚠ same type
- NIN p.Ala1755Val Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nin-p-val1230 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown